Lewis, Nathan E.

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., et al. (2011) · Nature Protocols

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 1,835

Deciphering cell–cell interactions and communication from gene expression

Armingol, E., Officer, A., Harismendy, O., & Lewis, N. E. (2021) · Nature Reviews Genetics

Bioinformatics and Genomic NetworksSingle-cell and spatial transcriptomics

Cited by 1,267

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

King, Z. A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J. A., Ebrahim, A., Palsson, B. O., & Lewis, N. E. (2016) · Nucleic Acids Research

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 938

The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line

Xu, X., Nagarajan, H., Lewis, N. E., Pan, S., Cai, Z., Liu, X., Chen, W., Xie, M., Wang, W., Hammond, S., et al. (2011) · Nature Biotechnology

Viral Infectious Diseases and Gene Expression in InsectsFungal and yeast genetics research

Cited by 785

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

Lewis, N. E., Nagarajan, H., & Palsson, B. O. (2012) · Nature Reviews Microbiology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 779

MEMOTE for standardized genome-scale metabolic model testing

Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., et al. (2020) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 509

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

Lewis, N. E., Liu, X., Li, Y., Nagarajan, H., Yerganian, G., O'Brien, E., Bordbar, A., Roth, A. M., Rosenbloom, J., Bian, C., et al. (2013) · Nature Biotechnology

Viral Infectious Diseases and Gene Expression in InsectsGenomics and Phylogenetic Studies

Cited by 380

Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions

Shen, J. P., Zhao, D., Sasik, R., Luebeck, J., Birmingham, A., Bojorquez-Gomez, A., Licon, K., Klepper, K., Pekin, D., Beckett, A. N., et al. (2017) · Nature Methods

CRISPR and Genetic EngineeringChromatin Remodeling and Cancer

Cited by 359

The ASD Living Biology: from cell proliferation to clinical phenotype

Courchesne, E., Pramparo, T., Gazestani, V. H., Lombardo, M. V., Pierce, K., & Lewis, N. E. (2019) · Molecular Psychiatry

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 333

Recon 2.2: from reconstruction to model of human metabolism

Swainston, N., Smallbone, K., Hefzi, H., Dobson, P. D., Brewer, J., Hanscho, M., Zielinski, D. C., Ang, K. S., Gardiner, N. J., Gutierrez, J. M., et al. (2016) · Metabolomics

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 285

Network Context and Selection in the Evolution to Enzyme Specificity

Nam, H., Lewis, N. E., Lerman, J. A., Lee, D.-H., Chang, R. L., Kim, D., & Palsson, B. O. (2012) · Science

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 277

In silico method for modelling metabolism and gene product expression at genome scale

Lerman, J. A., Hyduke, D. R., Latif, H., Portnoy, V. A., Lewis, N. E., Orth, J. D., Schrimpe-Rutledge, A. C., Smith, R. D., Adkins, J. N., Zengler, K., et al. (2012) · Nature Communications

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 266

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

Conrad, T. M., Frazier, M., Joyce, A. R., Cho, B.-K., Knight, E. M., Lewis, N. E., Landick, R., & Palsson, B. Ø. (2010) · Proceedings of the National Academy of Sciences

Bacterial Genetics and BiotechnologyEvolution and Genetic Dynamics

Cited by 241

Proteomic analysis of Chinese hamster ovary cells

Baycin-Hizal, D., Tabb, D. L., Chaerkady, R., Chen, L., Lewis, N. E., Nagarajan, H., Sarkaria, V., Kumar, A., Wolozny, D., Colao, J., et al. (2012) · Journal of Proteome Research

Viral Infectious Diseases and Gene Expression in InsectsAdvanced Proteomics Techniques and Applications

Cited by 178

The emerging CHO systems biology era: harnessing the ‘omics revolution for biotechnology

Kildegaard, H. F., Baycin-Hizal, D., Lewis, N. E., & Betenbaugh, M. J. (2013) · Current Opinion in Biotechnology

Viral Infectious Diseases and Gene Expression in InsectsMicrobial Metabolic Engineering and Bioproduction

Cited by 165

CRISPR/Cas9-mediated genome engineering of CHO cell factories: application and perspectives

Lee, J. S., Grav, L. M., Lewis, N. E., & Faustrup Kildegaard, H. (2015) · Biotechnology Journal

Viral Infectious Diseases and Gene Expression in InsectsCRISPR and Genetic Engineering

Cited by 117

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp, O., MacDonald, M. L., Li, S., Dhiman, H., Polson, S., Griep, S., Heffner, K., Hernandez, I., Brinkrolf, K., Jadhav, V., et al. (2018) · Biotechnology and Bioengineering

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 107

Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers

Pramparo, T., Lombardo, M. V., Campbell, K., Barnes, C. C., Marinero, S., Solso, S., Young, J., Mayo, M., Dale, A., Ahrens‐Barbeau, C., et al. (2015) · Molecular Systems Biology

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 88

The evolution of genome-scale models of cancer metabolism

Lewis, N. E., & Abdel-Haleem, A. M. (2013) · Frontiers in Physiology

Microbial Metabolic Engineering and BioproductionCancer, Hypoxia, and Metabolism

Cited by 87

Do genome-scale models need exact solvers or clearer standards?

Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A. P., Chang, R. L., Dräger, A., Famili, I., Feist, A. M., Fleming, R. M., et al. (2015) · Molecular Systems Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 57

JSBML 1.0: providing a smorgasbord of options to encode systems biology models

Rodriguez, N., Thomas, A., Watanabe, L., Vazirabad, I. Y., Kofia, V., Gómez, H. F., Mittag, F., Matthes, J., Rudolph, J., Wrzodek, F., et al. (2015) · Bioinformatics

Gene Regulatory Network AnalysisScientific Computing and Data Management

Cited by 37

The role of cellular objectives and selective pressures in metabolic pathway evolution

Nam, H., Conrad, T. M., & Lewis, N. E. (2011) · Current Opinion in Biotechnology

Microbial Metabolic Engineering and BioproductionEvolution and Genetic Dynamics

Cited by 32

Resource allocation in mammalian systems

Baghdassarian, H. M., & Lewis, N. E. (2024) · Biotechnology Advances

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 17

Resource Allocation in Mammalian Systems

Baghdassarian, H., & Lewis, N. (2023) · Biotechnology Advances

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 17